Variant report

Variant	rs4314161
Chromosome Location	chr3:118941098-118941099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:118940717-118941175	MCF-7	breast:	n/a	n/a
2	GATA3	chr3:118940650-118941195	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr3:118940716-118941341	MCF-7	breast:	n/a	n/a
4	CEBPB	chr3:118940656-118941123	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:118938238..118941184-chr3:118954679..118957762,3	K562	blood:
2	chr3:118939426..118941672-chr3:118946174..118948515,2	MCF-7	breast:
3	chr3:118939288..118941901-chr3:119040506..119042360,2	MCF-7	breast:
4	chr3:118936929..118943025-chr3:118955744..118960820,7	K562	blood:
5	chr3:118940569..118944138-chr3:118958769..118961318,3	K562	blood:
6	chr3:118938773..118941119-chr3:118950932..118953396,2	K562	blood:
7	chr3:118864134..118864841-chr3:118940785..118941535,2	MCF-7	breast:

No data

Variant related genes	Relation type
B4GALT4-AS1	TF binding region
ENSG00000121578	Chromatin interaction
ENSG00000144847	Chromatin interaction
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11707683	0.84[CEU][hapmap]
rs12630690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12632242	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs12637159	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13077850	0.94[EUR][1000 genomes]
rs13078534	0.94[EUR][1000 genomes]
rs13098335	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1584398	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2594728	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2594729	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34549395	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35625431	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806697	0.84[GIH][hapmap]
rs41271389	0.93[EUR][1000 genomes]
rs4234657	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4422293	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4422294	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4528932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547690	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4591498	1.00[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4603947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687841	0.82[TSI][hapmap]
rs55651430	0.94[EUR][1000 genomes]
rs6438504	1.00[CEU][hapmap];0.84[CHD][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs6438508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6438510	0.82[TSI][hapmap]
rs67180858	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67395904	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6778091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7610070	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs7612800	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs7612846	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs7622158	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv591362	chr3:118906442-118948155	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4314161	B4GALT4	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118924400-118959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:118924600-118945600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:118927000-118943200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:118927000-118952600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:118927000-118953800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:118927000-118953800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:118927200-118943000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:118927200-118953800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:118927200-118955200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:118927400-118941200	Strong transcription	Placenta	Placenta
11	chr3:118927400-118950200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:118927400-118953000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:118927600-118952400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:118927800-118943400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:118927800-118956400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:118928000-118943000	Strong transcription	Fetal Muscle Leg	muscle
17	chr3:118928000-118955600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:118928200-118943200	Strong transcription	Fetal Stomach	stomach
19	chr3:118928200-118943400	Strong transcription	Adipose Nuclei	Adipose
20	chr3:118928200-118951000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:118928800-118950000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:118929000-118943000	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:118929000-118943200	Strong transcription	Left Ventricle	heart
24	chr3:118929000-118943600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:118929000-118944200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:118929200-118956200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:118929200-118956200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:118929200-118956400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:118929200-118956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:118929400-118943000	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr3:118930000-118943000	Strong transcription	Stomach Smooth Muscle	stomach
32	chr3:118930000-118943600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:118930000-118949800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:118930000-118955400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:118930200-118943600	Strong transcription	HMEC	breast
36	chr3:118930200-118955800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:118930200-118958400	Weak transcription	Hela-S3	cervix
38	chr3:118930400-118943400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:118930800-118942400	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr3:118931600-118957400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:118931800-118946400	Genic enhancers	A549	lung
42	chr3:118932000-118941800	Weak transcription	Psoas Muscle	Psoas
43	chr3:118932200-118941400	Weak transcription	Fetal Kidney	kidney
44	chr3:118932600-118955800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:118933800-118942800	Strong transcription	Ovary	ovary
46	chr3:118935600-118943000	Strong transcription	NHEK	skin
47	chr3:118935800-118943000	Strong transcription	Aorta	Aorta
48	chr3:118935800-118947600	Weak transcription	HUVEC	blood vessel
49	chr3:118936000-118941800	Genic enhancers	Fetal Intestine Small	intestine
50	chr3:118936000-118943000	Strong transcription	Esophagus	oesophagus

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